Variant report

Variant	rs4343339
Chromosome Location	chr17:17872589-17872590
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17852605..17855081-chr17:17872067..17874591,2	K562	blood:

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10048206	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11078403	0.90[EUR][1000 genomes]
rs11078404	0.96[EUR][1000 genomes]
rs11078405	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11078406	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11078407	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11078408	0.83[EUR][1000 genomes]
rs11650649	0.90[EUR][1000 genomes]
rs11650890	0.89[EUR][1000 genomes]
rs11656840	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11657773	0.84[EUR][1000 genomes]
rs11657845	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11869536	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11870660	0.82[EUR][1000 genomes]
rs11871899	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12452219	0.95[EUR][1000 genomes]
rs12452254	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12600546	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12603148	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2350977	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28428991	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4077198	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4077828	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4244602	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4257260	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4299203	0.82[EUR][1000 genomes]
rs4321247	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4341796	0.95[EUR][1000 genomes]
rs4413022	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4414547	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4470201	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4471742	0.83[EUR][1000 genomes]
rs4534911	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4553680	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4616340	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4925123	0.90[EUR][1000 genomes]
rs4925125	0.91[EUR][1000 genomes]
rs4925126	0.93[EUR][1000 genomes]
rs4925129	0.96[EUR][1000 genomes]
rs4925130	0.93[EUR][1000 genomes]
rs5002487	0.96[EUR][1000 genomes]
rs57728924	0.82[EUR][1000 genomes]
rs62064156	0.96[EUR][1000 genomes]
rs62064158	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62072049	0.84[EUR][1000 genomes]
rs6502619	0.89[EUR][1000 genomes]
rs6502622	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6502624	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6502625	0.87[EUR][1000 genomes]
rs6502626	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6502627	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6502629	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs66531105	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67253360	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7207043	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7207395	0.95[EUR][1000 genomes]
rs7208190	0.93[EUR][1000 genomes]
rs7213225	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7214002	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7214536	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7219320	0.82[EUR][1000 genomes]
rs7222480	0.96[EUR][1000 genomes]
rs7224815	0.81[EUR][1000 genomes]
rs7503334	0.89[EUR][1000 genomes]
rs8065416	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8065563	0.89[EUR][1000 genomes]
rs8065970	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8066982	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8068175	0.82[EUR][1000 genomes]
rs8068820	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8070128	0.92[EUR][1000 genomes]
rs8070722	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8070748	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8073001	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8075965	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8076747	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8077338	0.82[EUR][1000 genomes]
rs8077530	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8078105	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8078138	0.95[EUR][1000 genomes]
rs8078583	0.95[EUR][1000 genomes]
rs8080061	0.80[EUR][1000 genomes]
rs8080823	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs950966	0.90[EUR][1000 genomes]
rs9635697	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9635698	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9890341	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9904163	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9905284	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9907287	0.80[EUR][1000 genomes]
rs9908017	0.80[EUR][1000 genomes]
rs9908832	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9912895	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9913724	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9914127	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv907766	chr17:17682484-17957348	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
5	nsv482879	chr17:17802463-17989273	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv510701	chr17:17850474-17955485	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4343339	SREBF1	cis	Whole Blood	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17862200-17874000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr17:17862400-17874200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr17:17863400-17874000	Weak transcription	NH-A	brain
4	chr17:17863600-17873800	Weak transcription	HSMMtube	muscle
5	chr17:17863800-17872800	Weak transcription	Brain Germinal Matrix	brain
6	chr17:17863800-17873800	Weak transcription	Fetal Muscle Leg	muscle
7	chr17:17863800-17873800	Weak transcription	Thymus	Thymus
8	chr17:17863800-17874400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr17:17864000-17873800	Weak transcription	HSMM	muscle
10	chr17:17864000-17874200	Weak transcription	Placenta	Placenta
11	chr17:17864000-17874400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr17:17864000-17874400	Weak transcription	Pancreas	Pancrea
13	chr17:17864200-17873600	Weak transcription	NHEK	skin
14	chr17:17864200-17873800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr17:17864200-17873800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr17:17864200-17873800	Weak transcription	Fetal Intestine Large	intestine
17	chr17:17864200-17874000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr17:17864200-17874200	Weak transcription	Fetal Intestine Small	intestine
19	chr17:17864200-17874200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr17:17864400-17872800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr17:17864400-17872800	Weak transcription	A549	lung
22	chr17:17864400-17873800	Weak transcription	Stomach Mucosa	stomach
23	chr17:17864400-17874400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr17:17864600-17873800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr17:17865800-17873200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr17:17866600-17874400	Enhancers	Fetal Heart	heart
27	chr17:17866800-17874200	Weak transcription	K562	blood
28	chr17:17867000-17874000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr17:17867000-17874200	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr17:17867200-17874000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr17:17867400-17873800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr17:17867600-17872800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr17:17867600-17873800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr17:17867600-17873800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr17:17867600-17874200	Weak transcription	Fetal Kidney	kidney
36	chr17:17867800-17872600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr17:17868200-17874000	Weak transcription	NHLF	lung
38	chr17:17868400-17874200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr17:17868600-17872600	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr17:17868600-17874200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr17:17868800-17873800	Weak transcription	Liver	Liver
42	chr17:17868800-17874400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr17:17868800-17875000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr17:17869000-17873600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr17:17869000-17873800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr17:17869000-17873800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr17:17869000-17873800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr17:17869000-17873800	Weak transcription	Colon Smooth Muscle	Colon
49	chr17:17869000-17873800	Weak transcription	Esophagus	oesophagus
50	chr17:17869000-17873800	Weak transcription	Fetal Lung	lung

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